Using ImageJ (FiJi) to measure particles on SEM images

Introduction

This tutorial provides a step-by-step guide on how to use ImageJ (specifically the FIJI distribution) to measure particles in Scanning Electron Microscopy (SEM) images. Accurate particle measurement is crucial in various scientific fields, including materials science and geology, as it helps in analyzing the size, shape, and distribution of particles.

Step 1: Install FIJI

• Download FIJI from the official website: FIJI Download.
• Choose the version compatible with your operating system (Windows, macOS, Linux).
• Install the software by following the prompts in the installer.

Step 2: Open SEM Images in FIJI

• Launch FIJI after installation.
• To open an SEM image, go to File > Open.
• Navigate to the location of your SEM image file and select it.

Step 3: Convert Image to Grayscale

• If your SEM image is not in grayscale, convert it by going to Image > Type > 8-bit.
• This step ensures that the image is suitable for further analysis and measurement.

Step 4: Adjust Image Contrast

• Enhance the visibility of particles by adjusting the contrast.
• Go to Image > Adjust > Brightness/Contrast.
• Use the sliders to adjust the levels until the particles are clearly visible. Click Apply to apply changes.

Step 5: Thresholding the Image

• Set a threshold to distinguish particles from the background.
• Go to Image > Adjust > Threshold.
• Adjust the sliders to highlight the particles while minimizing background noise. Ensure that all particles are highlighted in red.
• Click Apply to set the threshold.

Step 6: Analyze Particles

• To measure the particles, go to Analyze > Analyze Particles.

In the dialog box, set the following options

• Size: Enter size limits (e.g., 0-Infinity) to filter out very small or large particles.
• Show: Select "Outline" to visualize the measured particles on the image.
• Check options like "Display Results" and "Clear Results" if desired.
• Click OK to perform the analysis.

Step 7: Review Measurement Results

• After analysis, a results table will pop up displaying measurements such as area, perimeter, and circularity for each particle.
• Review the data to ensure it meets your expectations. You can export the data by going to File > Save As > Text Image.

Step 8: Save Your Processed Image

• To save the analyzed SEM image, go to File > Save As.
• Choose the desired file format (e.g., TIFF, JPEG) and save it to your preferred location.

Conclusion

In this tutorial, you learned how to use FIJI to measure particles in SEM images through a series of clear steps. From installing the software to analyzing particles and saving your results, these skills will enhance your ability to perform quantitative analysis in your research. For further exploration, consider experimenting with different image types or advanced analysis plugins available in FIJI.